You are here

Unsolved

The problem hasn't been solved

Problem with match on enzdes

Category: 
Enzyme Design

Hi all! I am attempting my very first enzyme design campaign and running into issues with matching. I generated a cstfile from averaging native pdb measurements within a family, and am trying to match my theozyme (a new substrate - LFF) to one representative structure as a test (PDB ID: 5nci chain A).

When I run:

Post Situation: 

Extracting a part of a silent file as another silent file

Category: 
Docking

Dear all,

I generated a silent file as a result of a docking refinement with FlexPepDock. I want to anaylize the top 10% of the solutions (1000 decoys) and cluster them.

First, I extracted the top 10% by sorting the I_sc with:

sort -n -k2 example_score_file.sc | head -n 1000 | awk '{print $2 "\t" $25 "\t" $NF}' > score_I-sc_tag.dat

Post Situation: 

FlexPepDock bug? Constraints do not appear in total_score?

Category: 
Constraints

Hi, looking for some help,

It appears that constraints do not contribute to the final score output when running the FlexPepDock ab initio protocol.

I am getting docking samples that should yield score penalties >1000 under the provided distance constraints (AtomPair FLAT_HARMONIC). However, the scorefile reports numbers consistent with the score absent of penalties (approx -550, for a protein length 300 and peptide length 5).

I provide the constraints file with the flag -constraints:cst_file

Post Situation: 

FlexPepDock ab initio: behavior without fragment files

Category: 
Docking

Hi there,

I've noticed that the FlexPepDock ab initio protocol will run even if fragments aren't specified. It also appears during these runs that the peptide backbone is flexible, varying between samples.

When no fragments are specified, what does the FlexPepDock application do to ab initio model peptides exactly?

Is there a 'default' set of fragments?

Thank you!

Nathan

Post Situation: 

tarball not correct for 3.13

Category: 
Compilation

Hi,

I just downloaded the 3.13 tarball (precompiled binaries) and when I extracted it, the directory structure says it's rosetta_bin_linux_2021.16.61629_bundle (the previous version).  Additionally, the md5sum values for all of the tarballs also point to 2021.16.61629.  Can you upload the 3.13 version? 

Best,

Ken

Post Situation: 

Less silly way to get number of iterations of Relax

Category: 
Scoring

Currently to get the number of iterations a mover, such as FastRelax does, I enable the dump_trajectory scoretype and count the models in the PDBs (code below).

This seems very very weird way of doing this, so I was wondering if there is a less silly way of doing this?

Also, is there a direct way to open a multimodel file say to get the scores of each? (Rather than extracting the models, writing to file, reading them into PyRosetta and scoring them).

Post Situation: 

Cereal

Category: 
Compilation

The compiled downloads of pyrosetta from Rosetta commons* aren't '--serialization' builds.

* I was going to doublecheck but https://www.rosettacommons.org/software/license-and-download is giving me a 404 for PyRosetta.

Is there any disadavantage in this build one should be wary of? Like slower, segfault-y-er, lacking other features etc. 
The fact that it is not one of the options makes me think there may be, hence my asking.

Post Situation: 

Pages

Subscribe to RSS - Unsolved